Read data

source("scripts/myRLib.R")
xt <- read.table("output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/xt.assoc.logistic", 
    header = T)
xt$SNP <- as.character(xt$SNP)
xt <- xt[order(xt$SNP), ]
yi <- read.table("output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/yi.logistic.assoc", 
    header = T)
xtyi.files <- strsplit("output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/xtyi_LDpred_p1.0000e+00.assoc.logistic:output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/xtyi_LDpred_p3.0000e-01.assoc.logistic:output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/xtyi_LDpred_p1.0000e-01.assoc.logistic:output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/xtyi_LDpred_p3.0000e-02.assoc.logistic:output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/xtyi_LDpred_p1.0000e-02.assoc.logistic:output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/xtyi_LDpred_p3.0000e-03.assoc.logistic:output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/xtyi_LDpred_p1.0000e-03.assoc.logistic:output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/xtyi_LDpred_p3.0000e-04.assoc.logistic:output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/xtyi_LDpred_p1.0000e-04.assoc.logistic", 
    ":")[[1]]
ps <- strsplit("1:0.3:0.1:0.03:0.01:0.003:0.001:0.0003:0.0001", 
    ":")[[1]]

Plots

for (i in 1:length(xtyi.files)) {
    xtyi <- read.table(xtyi.files[i], header = T)
    xtyi$SNP <- as.character(xtyi$SNP)
    xtyi <- xtyi[order(xtyi$SNP), ]
    p <- ps[i]
    cat("##", "Cutoff =", p, "\n")
    cat("\n")
    cat("\n")
    cat("Filename is", as.character(yi[i, 1]))
    cat("\n")
    pander(yi[i, 2:ncol(yi)])
    qqplot(-log10((1:length(xt$P))/length(xt$P)), -log10(xt$P), 
        main = "QQplot - Gi: Y ~ Gi", xlab = "-log10 expected pval", 
        ylab = "-log10 observed pval")
    abline(a = 0, b = 1, col = "red")
    qqplot(-log10((1:length(xtyi[xtyi$TEST == "ADD", "P"]))/length(xtyi[xtyi$TEST == 
        "ADD", "P"])), -log10(xtyi[xtyi$TEST == "ADD", "P"]), 
        main = "QQplot - Gi: Y ~ Gi + I", xlab = "-log10 expected pval", 
        ylab = "-log10 observed pval")
    abline(a = 0, b = 1, col = "red")
    hist(log(xtyi[xtyi$TEST == "PRS", "OR"]), main = "Hist - I: Y ~ Gi + I", 
        xlab = "OR")
    abline(v = yi[i, "prs.estmate"], col = "red")
    abline(v = yi[i, "prs.estmate"] - yi[i, "prs.std"], col = "red")
    abline(v = yi[i, "prs.estmate"] + yi[i, "prs.std"], col = "red")
    plot(xt$P, xtyi[xtyi$TEST == "ADD", "P"], main = "P-value of Gi: Gi + I vs Gi", 
        xlab = "Gi", ylab = "Gi + I")
    cat("\n")
    cat("\n")
}

Cutoff = 1

Filename is output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/covar_LDpred_p1.0000e+00.txt

intercept.estmate intercept.std intercept.pval prs.estmate prs.std prs.pval
-0.5418 0.03137 8.018e-67 0.04412 0.01577 0.005155

Cutoff = 0.3

Filename is output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/covar_LDpred_p3.0000e-01.txt

  intercept.estmate intercept.std intercept.pval prs.estmate prs.std prs.pval
2 -0.5656 0.03476 1.633e-59 0.03532 0.01284 0.005935

Cutoff = 0.1

Filename is output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/covar_LDpred_p1.0000e-01.txt

  intercept.estmate intercept.std intercept.pval prs.estmate prs.std prs.pval
3 -0.5531 0.03344 1.993e-61 0.02671 0.01108 0.01594

Cutoff = 0.03

Filename is output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/covar_LDpred_p3.0000e-02.txt

  intercept.estmate intercept.std intercept.pval prs.estmate prs.std prs.pval
4 -0.5846 0.04352 3.835e-41 0.02307 0.01096 0.0354

Cutoff = 0.01

Filename is output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/covar_LDpred_p1.0000e-02.txt

  intercept.estmate intercept.std intercept.pval prs.estmate prs.std prs.pval
5 -0.6643 0.06546 3.349e-24 0.02777 0.01106 0.012

Cutoff = 0.003

Filename is output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/covar_LDpred_p3.0000e-03.txt

  intercept.estmate intercept.std intercept.pval prs.estmate prs.std prs.pval
6 -0.6481 0.06936 9.291e-21 0.02437 0.01176 0.03823

Cutoff = 0.001

Filename is output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/covar_LDpred_p1.0000e-03.txt

  intercept.estmate intercept.std intercept.pval prs.estmate prs.std prs.pval
7 -0.6485 0.07401 1.927e-18 0.0237 0.01235 0.055

Cutoff = 0.0003

Filename is output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/covar_LDpred_p3.0000e-04.txt

  intercept.estmate intercept.std intercept.pval prs.estmate prs.std prs.pval
8 -0.6515 0.08246 2.761e-15 0.02208 0.01277 0.08387

Cutoff = 0.0001

Filename is output-direction_XT_YI/UKBB_wbc__wtccc_crohn__wtccc_ctrl/covar_LDpred_p1.0000e-04.txt

  intercept.estmate intercept.std intercept.pval prs.estmate prs.std prs.pval
9 -0.6468 0.08097 1.37e-15 0.02247 0.0132 0.08867